[gmx-users] problem during energy minimization

soumadwip ghosh soumadwipghosh at gmail.com
Tue Dec 9 12:51:21 CET 2014

        I am simulating a double stranded DNA in presence of choline. I am
using CHARMM force field and GROMACS 4.5.6 for my simulations. I made the
choline molecule as suggested by justin using CGenFF and included in my
system by using -ci -nmol option of genbox. I am facing some problems in
the energy minimization step which is as follows-

Back Off! I just backed up emz.log to ./#emz.log.1#
Reading file emz.tpr, VERSION 4.5.6 (single precision)
Starting 80 threads
Making 3D domain decomposition 5 x 4 x 4

Back Off! I just backed up emz.trr to ./#emz.trr.1#

Back Off! I just backed up emz.edr to ./#emz.edr.1#

Steepest Descents:
   Tolerance (Fmax)   =  1.00000e+03
   Number of steps    =        50000

Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 1000

Double precision normally gives you higher accuracy.
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)

writing lowest energy coordinates.

Back Off! I just backed up emz.gro to ./#emz.gro.1#

Steepest Descents converged to machine precision in 331 steps,
but did not reach the requested Fmax < 1000.
Potential Energy  =  5.4556762e+08
Maximum force     =  4.0237480e+04 on atom 919
Norm of force     =  4.8998334e+02

NOTE: 7 % of the run time was spent communicating energies,
      you might want to use the -gcom option of mdrun

My minimization.mdp file is as follows-

; minim.mdp - used as input into grompp to generate em.tpr
; Parameters describing what to do, when to stop and what to save
integrator      = steep         ; Algorithm (steep = steepest descent
emtol           = 1000.0        ; Stop minimization when the maximum force
< 1000.0 kJ/mol/nm
emstep          = 0.01          ; Energy step size
nsteps          = 50000         ; Maximum number of (minimization) steps to

; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist         = 1             ; Frequency to update the neighbor list and
long range forces
ns_type         = grid          ; Method to determine neighbor list
(simple, grid)
rlist           = 1.0           ; Cut-off for making neighbor list (short
range forces)
coulombtype     = PME           ; Treatment of long range electrostatic
rcoulomb        = 1.0           ; Short-range electrostatic cut-off
rvdw            = 1.0           ; Short-range Van der Waals cut-off
pbc             = xyz           ; Periodic Boundary Conditions (yes/no)

I read about 'blowing up' of the system but I dont know how to use double
precission GROMACS. I cant figure out what the problem is. Is there
anything wrong with the .mdp file? Is there anything wrong with my initial
and solvated configurations? If not what is the way to get rid of this

Thanks for your help and time in advance.

Soumadwip Ghosh
Research Fellow
Indian Institute of Technology, Bombay

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